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Yorodumi- PDB-4ud6: Structure of methylviologen-treated anaerobically purified D. fru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ud6 | ||||||
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Title | Structure of methylviologen-treated anaerobically purified D. fructosovorans NiFe-hydrogenase | ||||||
Components |
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Keywords | OXIDOREDUCTASE / NIFE-HYDROGENASE / NI-SIB STATE / NI-C STATE | ||||||
Function / homology | Function and homology information cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Volbeda, A. / Martin, L. / Liebgott, P.-P. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: Metallomics / Year: 2015 Title: [NiFe]-hydrogenases revisited: nickel-carboxamido bond formation in a variant with accrued O2-tolerance and a tentative re-interpretation of Ni-SI states. Authors: Volbeda, A. / Martin, L. / Liebgott, P.P. / De Lacey, A.L. / Fontecilla-Camps, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ud6.cif.gz | 954.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ud6.ent.gz | 792.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ud6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ud6_validation.pdf.gz | 529.1 KB | Display | wwPDB validaton report |
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Full document | 4ud6_full_validation.pdf.gz | 540.3 KB | Display | |
Data in XML | 4ud6_validation.xml.gz | 101.3 KB | Display | |
Data in CIF | 4ud6_validation.cif.gz | 149.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/4ud6 ftp://data.pdbj.org/pub/pdb/validation_reports/ud/4ud6 | HTTPS FTP |
-Related structure data
Related structure data | 4ud2C 4ue2C 4ue6C 4ueqC 4uewC 2frvS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 2 types, 6 molecules ABCQRS
#1: Protein | Mass: 28347.314 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria) References: UniProt: E1K248, cytochrome-c3 hydrogenase #2: Protein | Mass: 59788.328 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria) References: UniProt: E1K247, cytochrome-c3 hydrogenase |
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-Non-polymers , 7 types, 1922 molecules
#3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.2 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: IN GLOVEBOX, PH 6.6, 293K, PEG6000, MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 8, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→20 Å / Num. obs: 131493 / % possible obs: 99.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.12→2.2 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.8 / % possible all: 98 |
-Processing
Software | Name: REFMAC / Version: 5.8.0071 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FRV Resolution: 2.12→19.99 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.934 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.834 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→19.99 Å
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Refine LS restraints |
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